[2024-01-24 11:43:53,276] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:53,284] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:53,285] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dcacdaa-5f4f-4881-9e50-a9b992dde480/dqc_reference
[2024-01-24 11:43:54,561] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:54,562] [INFO] Task started: Prodigal
[2024-01-24 11:43:54,562] [INFO] Running command: gunzip -c /var/lib/cwl/stg8bc56af3-064c-4179-a511-685045542621/GCF_024125445.1_ASM2412544v1_genomic.fna.gz | prodigal -d GCF_024125445.1_ASM2412544v1_genomic.fna/cds.fna -a GCF_024125445.1_ASM2412544v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:05,031] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:05,032] [INFO] Task started: HMMsearch
[2024-01-24 11:44:05,032] [INFO] Running command: hmmsearch --tblout GCF_024125445.1_ASM2412544v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dcacdaa-5f4f-4881-9e50-a9b992dde480/dqc_reference/reference_markers.hmm GCF_024125445.1_ASM2412544v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:05,287] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:05,288] [INFO] Found 6/6 markers.
[2024-01-24 11:44:05,324] [INFO] Query marker FASTA was written to GCF_024125445.1_ASM2412544v1_genomic.fna/markers.fasta
[2024-01-24 11:44:05,325] [INFO] Task started: Blastn
[2024-01-24 11:44:05,325] [INFO] Running command: blastn -query GCF_024125445.1_ASM2412544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dcacdaa-5f4f-4881-9e50-a9b992dde480/dqc_reference/reference_markers.fasta -out GCF_024125445.1_ASM2412544v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:05,894] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:05,897] [INFO] Selected 17 target genomes.
[2024-01-24 11:44:05,897] [INFO] Target genome list was writen to GCF_024125445.1_ASM2412544v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:05,903] [INFO] Task started: fastANI
[2024-01-24 11:44:05,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bc56af3-064c-4179-a511-685045542621/GCF_024125445.1_ASM2412544v1_genomic.fna.gz --refList GCF_024125445.1_ASM2412544v1_genomic.fna/target_genomes.txt --output GCF_024125445.1_ASM2412544v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:17,006] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:17,006] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dcacdaa-5f4f-4881-9e50-a9b992dde480/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:17,007] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dcacdaa-5f4f-4881-9e50-a9b992dde480/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:17,012] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:17,013] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:17,013] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Sporolactobacillus shoreicorticis	strain=LMG 29111	GCA_024125445.1	1923877	1923877	type	True	100.0	1436	1438	95	conclusive
Sporolactobacillus nakayamae	strain=ATCC 700379	GCA_900113325.1	269670	269670	type	True	80.7369	619	1438	95	below_threshold
Sporolactobacillus laevolacticus	strain=DSM 442	GCA_000497245.1	33018	33018	type	True	78.9947	369	1438	95	below_threshold
Sporolactobacillus shoreae	strain=BK92	GCA_004684935.1	1465501	1465501	type	True	78.8071	173	1438	95	below_threshold
Sporolactobacillus pectinivorans	strain=GD201205	GCA_002802965.1	1591408	1591408	type	True	77.7405	150	1438	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:17,014] [INFO] DFAST Taxonomy check result was written to GCF_024125445.1_ASM2412544v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:17,015] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:17,015] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:17,015] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dcacdaa-5f4f-4881-9e50-a9b992dde480/dqc_reference/checkm_data
[2024-01-24 11:44:17,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:17,058] [INFO] Task started: CheckM
[2024-01-24 11:44:17,058] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024125445.1_ASM2412544v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024125445.1_ASM2412544v1_genomic.fna/checkm_input GCF_024125445.1_ASM2412544v1_genomic.fna/checkm_result
[2024-01-24 11:44:52,514] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:52,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:52,533] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:52,533] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:52,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024125445.1_ASM2412544v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:52,533] [INFO] Task started: Blastn
[2024-01-24 11:44:52,534] [INFO] Running command: blastn -query GCF_024125445.1_ASM2412544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dcacdaa-5f4f-4881-9e50-a9b992dde480/dqc_reference/reference_markers_gtdb.fasta -out GCF_024125445.1_ASM2412544v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:53,292] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:53,297] [INFO] Selected 22 target genomes.
[2024-01-24 11:44:53,297] [INFO] Target genome list was writen to GCF_024125445.1_ASM2412544v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:53,311] [INFO] Task started: fastANI
[2024-01-24 11:44:53,311] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bc56af3-064c-4179-a511-685045542621/GCF_024125445.1_ASM2412544v1_genomic.fna.gz --refList GCF_024125445.1_ASM2412544v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024125445.1_ASM2412544v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:06,286] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:06,294] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:45:06,294] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_900113325.1	s__Sporolactobacillus nakayamae	80.7025	623	1438	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000497245.1	s__Sporolactobacillus laevolacticus	78.9947	369	1438	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684935.1	s__Sporolactobacillus shoreae	78.8065	173	1438	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802965.1	s__Sporolactobacillus pectinivorans	77.7334	149	1438	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004153195.1	s__Sporolactobacillus sp004153195	77.4411	113	1438	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004153165.1	s__Sporolactobacillus sp004153165	77.4214	110	1438	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004153225.1	s__Sporolactobacillus sp004153225	77.1039	78	1438	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543345.1	s__Sporolactobacillus sp900543345	76.9333	55	1438	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Sporolactobacillaceae;g__Sporolactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:06,296] [INFO] GTDB search result was written to GCF_024125445.1_ASM2412544v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:06,297] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:06,299] [INFO] DFAST_QC result json was written to GCF_024125445.1_ASM2412544v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:06,300] [INFO] DFAST_QC completed!
[2024-01-24 11:45:06,300] [INFO] Total running time: 0h1m13s